Persistent magnetoresistance effects in the phase-separated Pr0.65(Ca0.25Sr0.75)0.35MnO3/SrTiO3 and Pr0.65(Ca0.25Sr0.75)0.35MnO3/0.7PbMg1/3Nb2/3O3–0.3PbTiO3 heterostructures under a low magnetic field are investigated. It is observed that the persistent magnetoresistance effects decrease with increasing temperatures and the values for the heterostructures on 0.7Pb(Mg1/3Nb2/3)O3–0.3PbTiO3 and SrTiO3 substrates are about 86.6% and 33.2% at 40 K, respectively. More interestingly, the applied electric field on the 0.7PbMg1/3Nb2/3O3–0.3PbTiO3 substrate can suppress the persistent magnetoresistance effect, indicating that different energy landscapes can be dramatically modulated by the piezo-strain. These results are discussed in terms of the strain-induced competition in the ferromagnetic state and the charge-ordering phase by the energy scenario, which provide a promising approach for designing devices of electric-magnetic memories in all-oxide heterostructures.